Contacts of the helix formed by residues 7 - 20 (chain A) in PDB entry 4ZC3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 1.3 74.3 - - - +
8A PRO* 1.4 73.8 - - - +
9A LYS* 3.9 9.3 + - - +
10A GLN* 3.1 30.4 + - - +
11A GLU* 2.9 29.3 + - - +
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Residues in contact with PRO 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU 3.8 1.8 - - - +
7A SER* 1.4 90.7 - - - +
9A LYS* 1.3 56.0 + - - +
11A GLU* 3.5 10.9 - - + +
12A ARG* 2.9 28.9 + - - +
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A SER* 3.2 7.8 - - - +
8A PRO* 1.3 77.2 - - - +
10A GLN* 1.3 60.9 + - + +
12A ARG* 3.4 6.1 + - - +
13A PHE* 2.9 27.9 + - - +
31A ALA* 3.4 17.5 - - - +
32A GLY* 3.0 39.1 + - - -
33A TYR* 3.7 38.2 + - + +
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Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.2 3.8 + - - -
7A SER* 3.1 29.0 + - - +
9A LYS* 1.3 78.9 - - + +
11A GLU* 1.3 60.7 + - - +
13A PHE* 3.3 7.6 + - - +
14A ILE* 3.1 29.2 + - - +
33A TYR* 3.6 16.6 + - - +
45A ASN* 3.1 26.4 + - - +
48A LYS* 3.3 30.5 - - - +
51A ILE* 3.8 18.6 - - + +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.7 24.3 - - - +
7A SER 2.9 20.3 + - - +
8A PRO* 3.5 11.7 - - + +
10A GLN* 1.3 72.0 - - - +
12A ARG* 1.3 64.8 + - - +
14A ILE* 3.2 12.2 + - - +
15A GLU* 3.0 25.2 + - - +
54A ARG* 2.7 41.6 + - - -
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO 2.9 18.1 + - - +
9A LYS* 3.6 7.6 - - - +
10A GLN 3.4 0.2 - - - -
11A GLU* 1.3 75.8 - - - +
13A PHE* 1.3 57.7 + - - +
15A GLU* 3.2 10.8 + - - +
16A GLU* 2.6 62.6 + - + +
19A ILE* 6.1 0.4 - - - -
30A ALA* 3.5 17.2 + - - +
31A ALA* 3.7 21.4 + - + +
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Residues in contact with PHE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS 2.9 15.2 + - - +
10A GLN* 3.4 13.5 - - - +
11A GLU 3.2 0.4 - - - -
12A ARG* 1.3 75.5 - - - +
14A ILE* 1.3 61.4 + - - +
16A GLU* 3.2 2.9 + - - +
17A TYR* 2.8 41.0 + + + +
24A ALA* 3.5 32.3 - - + -
27A ALA* 3.8 6.5 - - + -
28A ALA* 3.8 20.2 - - - -
31A ALA* 3.6 10.9 - - + +
33A TYR* 4.5 1.8 - + + -
42A GLY* 3.7 28.9 - - - -
45A ASN* 3.7 32.5 - - + +
46A LEU* 4.2 7.2 - - + -
51A ILE* 4.2 19.7 - - + -
55A ILE* 5.1 2.5 - - + -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLN 3.1 18.9 + - - +
11A GLU* 3.2 17.7 + - - +
13A PHE* 1.3 79.2 - - + +
15A GLU* 1.3 64.4 + - + +
17A TYR* 3.3 11.7 + - - +
18A PHE* 3.4 25.3 - - + -
51A ILE* 3.7 39.0 - - + -
54A ARG* 3.7 35.9 - - + +
55A ILE* 4.4 17.5 - - + -
58A ARG* 4.6 18.8 - - + +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU 3.0 15.0 + - - +
12A ARG* 3.2 15.0 + - - +
14A ILE* 1.3 76.5 - - + +
16A GLU* 1.3 57.7 + - - +
18A PHE* 3.2 4.5 + - - +
19A ILE* 2.9 44.8 + - + +
58A ARG* 3.0 36.4 + - - +
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 2.6 64.0 + - + +
13A PHE 3.8 1.8 - - - +
15A GLU* 1.3 69.4 - - - +
17A TYR* 1.3 61.3 + - - +
19A ILE* 3.7 24.9 - - - +
20A ASN* 2.9 54.3 + - - +
27A ALA* 3.5 26.4 - - - +
30A ALA* 3.4 21.0 - - + +
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Residues in contact with TYR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 2.8 23.3 + + + +
14A ILE* 3.5 8.1 - - - +
15A GLU 3.2 0.2 - - - -
16A GLU* 1.3 79.6 - - - +
18A PHE* 1.3 72.3 + + - +
20A ASN 3.8 0.5 - - - -
21A ASP 3.5 1.4 + - - -
22A MET* 2.8 84.7 + - + +
23A ASN 4.9 0.7 - - - -
24A ALA* 4.2 22.4 - - + -
27A ALA* 3.4 8.9 - - + +
46A LEU* 3.4 30.2 - - + +
52A ARG* 4.9 3.1 + - - -
55A ILE* 3.9 38.1 - - + -
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.4 17.7 - - + -
15A GLU* 3.2 7.2 + - - +
17A TYR* 1.3 91.0 - + - +
19A ILE* 1.3 67.1 + - + +
20A ASN 3.3 0.9 + - - -
21A ASP* 3.3 13.7 + - - +
22A MET* 3.5 31.4 - - + +
55A ILE* 4.0 24.7 - - + -
58A ARG* 3.6 52.9 - - + +
59A LEU* 3.8 8.3 - - + -
62A ILE* 3.5 32.5 - - + -
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLU* 2.9 35.8 + - + +
16A GLU* 3.4 35.0 + - - +
18A PHE* 1.3 76.9 - - - +
20A ASN* 1.3 62.7 + - - +
21A ASP* 3.4 11.0 + - - +
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.9 52.2 + - - +
17A TYR 3.8 0.4 - - - +
19A ILE* 1.3 82.0 - - - +
21A ASP* 1.3 73.3 + - - +
22A MET 3.2 2.9 - - - -
23A ASN* 3.1 28.3 + - - +
26A LYS* 3.0 45.6 + - - +
27A ALA* 4.2 5.1 - - - +
30A ALA* 4.3 2.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il